BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy4383
(89 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 55.5 bits (132), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 24/40 (60%), Positives = 31/40 (77%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ G S+HKGYAF+Q+SN AR+A LGE+GR + GQTL
Sbjct: 53 GRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAGQTL 92
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/37 (62%), Positives = 30/37 (81%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
+HKGYAF+Q+SN AR+A LGE+GR + GQTL I+M
Sbjct: 60 VHKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM 96
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 21/40 (52%), Positives = 30/40 (75%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ +G S+HKG+AF+Q+ N +AR+A GEDGR + GQ L
Sbjct: 41 GKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAGQVL 80
Score = 49.3 bits (116), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 19/37 (51%), Positives = 28/37 (75%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
+HKG+AF+Q+ N +AR+A GEDGR + GQ L I++
Sbjct: 48 VHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL 84
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
G+AF++F +P DA A G DG+ + G + + + G
Sbjct: 38 GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTG 74
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+AF++F +P DA A G DG+ + G +
Sbjct: 38 GFAFVEFEDPRDAEDAVRGLDGKVICGSRV 67
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 26/41 (63%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAF 43
+G+AFI F NP DA++A +G+++ G+ + + K +F
Sbjct: 48 RGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF 88
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 36 SMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV---SYKLQYYNGCRYVSPT 86
S +G+AFI F NP DA++A +G+++ G+ + + K + +G R P
Sbjct: 45 SKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPA 98
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
G+AF++F +P DA A DGRT+ G + + + G
Sbjct: 111 GFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELSNG 147
Score = 33.1 bits (74), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLG 66
G+AF++F +P DA A DGRT+ G
Sbjct: 111 GFAFVEFEDPRDAADAVRDLDGRTLCG 137
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
G+AF++F +P DA A DGRT+ G + + + G
Sbjct: 111 GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 147
Score = 32.7 bits (73), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLG 66
G+AF++F +P DA A DGRT+ G
Sbjct: 111 GFAFVEFEDPRDAADAVRELDGRTLCG 137
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLVS 71
KGYA+++F NP +A A DG + GQ + +
Sbjct: 47 KGYAYVEFENPDEAEKALKHMDGGQIDGQEITA 79
Score = 33.1 bits (74), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYA+++F NP +A A DG + GQ +
Sbjct: 47 KGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G + I++ + FIQF NP R A E G+ L+
Sbjct: 48 GHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI 88
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 32.3 bits (72), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G + I++ + FIQF NP R A E G+ L+
Sbjct: 28 GHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLI 68
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 32.0 bits (71), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G + I++ + FIQF NP R A E G+ L+
Sbjct: 36 GHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLI 76
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 19/46 (41%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQF 46
+ + FIQF NP R A E G+ L + + A QF
Sbjct: 43 IKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQF 88
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G + I++ + FIQF NP R A E G+ L+
Sbjct: 48 GHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLI 88
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 31.2 bits (69), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+GYAFI++ + D SA DG+ + G+ + + + +G
Sbjct: 144 RGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
+GYAFI++ + D SA DG+ + G+ ++
Sbjct: 144 RGYAFIEYEHERDMHSAYKHADGKKIDGRRVL 175
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+G+AF++F + DA A DG + G+ L + M +
Sbjct: 112 RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 148
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AF++F + DA A DG + G+ L
Sbjct: 112 RGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 142
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 5 YAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+AF++F +P DA A G DG G L + +
Sbjct: 63 FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 97
Score = 29.6 bits (65), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 41 YAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+AF++F +P DA A G DG G L
Sbjct: 63 FAFVEFEDPRDAEDAVYGRDGYDYDGYRL 91
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
H+G+AF++F DA +A + + G+T+ +++ K
Sbjct: 48 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+G+AF++F DA +A + + G+T+
Sbjct: 48 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 79
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 30.4 bits (67), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
H+G+AF++F DA +A + + G+T+ +++ K
Sbjct: 46 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 83
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+G+AF++F DA +A + + G+T+
Sbjct: 46 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 77
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGI 35
+G+ F+ F N DA+ A + +G++V G+ + +
Sbjct: 54 RGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV 86
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+ F+ F N DA+ A + +G++V G+ +
Sbjct: 54 RGFGFVTFENIDDAKDAMMAMNGKSVDGRQI 84
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.0 bits (66), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMH 38
KGYAFI+F++ DA+ A + R + G+ + + +
Sbjct: 53 KGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ 88
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGYAFI+F++ DA+ A + R + G+ +
Sbjct: 53 KGYAFIEFASFEDAKEALNSCNKREIEGRAI 83
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+G+AF++F + DA A DG + G+ L + M +
Sbjct: 89 RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AF++F + DA A DG + G+ L
Sbjct: 89 RGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
H+G+AF++F DA +A + + G+T+ +++ K
Sbjct: 53 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 90
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+G+AF++F DA +A + + G+T+
Sbjct: 53 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 84
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 29.3 bits (64), Expect = 0.58, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+GYAFI++ + D SA DG+ + G+ + + + +G
Sbjct: 144 RGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181
Score = 26.9 bits (58), Expect = 3.1, Method: Composition-based stats.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
+GYAFI++ + D SA DG+ + G+ ++
Sbjct: 144 RGYAFIEYEHERDMHSAYKHADGKKIDGRRVL 175
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+ YAF+ FSN DA A +G+ + G + +++ K
Sbjct: 51 RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 87
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 28.9 bits (63), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
H+G+AF++F DA +A + + G+T+ +++
Sbjct: 43 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 78
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+G+AF++F DA +A + + G+T+
Sbjct: 43 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 74
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 28.9 bits (63), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
H+G+AF++F DA +A + + G+T+ +++
Sbjct: 104 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+G+AF++F DA +A + + G+T+
Sbjct: 104 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 135
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 29 LGQTLGISM--HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLVSY 72
GQ + I + KGY+F++FS A A + +G T+ G + Y
Sbjct: 49 FGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY 94
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY+F++FS A A + +G T+ G +
Sbjct: 60 EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNP 49
+G+AF++F + DA+ A DG + G+ L + + + Y S P
Sbjct: 55 RGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVAR-YGRRDLSGP 100
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AF++F + DA+ A DG + G+ L
Sbjct: 55 RGFAFVRFHDRRDAQDAEAAMDGAELDGREL 85
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
KG+ F+ FS+P +A A +GR V + L +++ +
Sbjct: 55 KGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ 91
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+ F+ FS+P +A A +GR V + L
Sbjct: 55 KGFGFVCFSSPEEATKAVTEMNGRIVATKPL 85
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 18 SACLGEDGRTVL---GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+AC ++ R++ G+ + + K YAF+ DA++A +G+ V G+ +
Sbjct: 19 AACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKGKRI 73
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
K YAF+ DA++A +G+ V G+ + + +
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL 77
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 13/85 (15%)
Query: 10 FSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
F + D S L D + GQ+LG Y F+ +S+P+DA A +G + +T+
Sbjct: 25 FGSIGDIESCKLVRD--KITGQSLG------YGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 70 -VSYKLQYYNGCR----YVSPTPTT 89
VSY R YVS P T
Sbjct: 77 KVSYARPSSASIRDANLYVSGLPKT 101
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
GY F+ +S+P+DA A +G + +T+ +S
Sbjct: 47 GYGFVNYSDPNDADKAINTLNGLKLQTKTIKVS 79
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
GY F+ +S+P+DA A +G + +T+ +S
Sbjct: 47 GYGFVNYSDPNDADKAINTLNGLKLQTKTIKVS 79
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 9/64 (14%)
Query: 10 FSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
F + D S L D + GQ+LG Y F+ +S+P+DA A +G + +T+
Sbjct: 25 FGSIGDIESCKLVRD--KITGQSLG------YGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 70 -VSY 72
VSY
Sbjct: 77 KVSY 80
>pdb|3KJE|A Chain A, Empty State Of Cooc1
pdb|3KJG|A Chain A, Adp-Bound State Of Cooc1
pdb|3KJG|B Chain B, Adp-Bound State Of Cooc1
pdb|3KJH|A Chain A, Zn-Bound State Of Cooc1
pdb|3KJI|A Chain A, Zn And Adp Bound State Of Cooc1
pdb|3KJI|B Chain B, Zn And Adp Bound State Of Cooc1
Length = 254
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 24 DGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVL 65
D + LGQTLG+S+ + YA D G+ G +L
Sbjct: 37 DPDSCLGQTLGLSIEEAYAITPLIEMKDEIREKTGDGGLLIL 78
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
Length = 109
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KGY +++ +A++A G +G+ ++GQ + +
Sbjct: 49 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 49 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 79
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KGY +++ +A++A G +G+ ++GQ + +
Sbjct: 64 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 64 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 94
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KGY +++ +A++A G +G+ ++GQ + +
Sbjct: 49 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
Score = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 49 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 79
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KGY +++ +A++A G +G+ ++GQ + +
Sbjct: 49 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 49 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 79
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KGY +++ +A++A G +G+ ++GQ + +
Sbjct: 51 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 85
Score = 25.8 bits (55), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 51 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 81
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KGY +++ +A++A G +G+ ++GQ + +
Sbjct: 65 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 65 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 95
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 34 GISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ + G+ F+++ P A+ A G TV G L
Sbjct: 45 GVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKL 80
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KGYA +++ A +A +G ++GQT+ +
Sbjct: 68 KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 102
>pdb|1NMA|N Chain N, N9 Neuraminidase Complexes With Antibodies Nc41 And Nc10:
Empirical Free-Energy Calculations Capture Specificity
Trends Observed With Mutant Binding Data
Length = 388
Score = 25.8 bits (55), Expect = 6.4, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 23 EDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
+ G T LG+T+ I+ GY ++ N A + R GQT+V
Sbjct: 275 DGGNTWLGRTISIASRSGYEMLKVPN------ALTDDKSRPTQGQTIV 316
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
+G+AF+ F N DA+ A +G + G+ + +S
Sbjct: 57 RGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 25.4 bits (54), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
+GY F+ F++ DA++A G+ + G+ L I+
Sbjct: 129 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 25.4 bits (54), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
+GY F+ F++ DA++A G+ + G+ L I+
Sbjct: 43 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 76
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 25.4 bits (54), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KGYA +++ A +A +G ++GQT+ +
Sbjct: 114 KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.137 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,959,508
Number of Sequences: 62578
Number of extensions: 104281
Number of successful extensions: 376
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 45
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 285
Number of HSP's gapped (non-prelim): 95
length of query: 89
length of database: 14,973,337
effective HSP length: 56
effective length of query: 33
effective length of database: 11,468,969
effective search space: 378475977
effective search space used: 378475977
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)